LOCUS       NZ_CP063507             6044 bp    DNA     circular CON 17-JUN-2023
DEFINITION  Escherichia coli strain EH09-18-41 plasmid pEH09-18-41_4, complete
            sequence.
ACCESSION   NZ_CP063507
VERSION     NZ_CP063507.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16387495
            Assembly: GCF_016944715.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6044)
  AUTHORS   Moser,A.I., Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Complete genome and plasmid sequences of MDR Escherichia coli from
            local people and environmental sources in Laos
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6044)
  AUTHORS   Moser,A.I., Campos-Madueno,E.I. and Endimiani,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-OCT-2020) Institute for Infectious Diseases,
            University of Bern, Friedbuehlstrasse 51, Bern 3001, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.7.1
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 397x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/17/2023 06:32:02
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,054
            CDSs (total)                      :: 4,930
            Genes (coding)                    :: 4,724
            CDSs (with protein)               :: 4,724
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 206
            CDSs (without protein)            :: 206
            Pseudo Genes (ambiguous residues) :: 0 of 206
            Pseudo Genes (frameshifted)       :: 57 of 206
            Pseudo Genes (incomplete)         :: 149 of 206
            Pseudo Genes (internal stop)      :: 32 of 206
            Pseudo Genes (multiple problems)  :: 34 of 206
            Pseudo Genes (short protein)      :: 4 of 206
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP063507.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..6044
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="EH09-18-41"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pEH09-18-41_4"
                     /geo_loc_name="Laos"
                     /collection_date="2018"
                     /collected_by="Institute for Infectious Diseases Bern"
     gene            join(5220..6044,1..21)
                     /locus_tag="IQS19_RS25290"
     CDS             join(5220..6044,1..21)
                     /locus_tag="IQS19_RS25290"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_251326744.1"
                     /translation="MIVKFHARGKGGGSGPVDYLLGRERNREGATVLQGNPEEVRELID
                     ATPFAKKYTSGVLSFAEKELPPGGREKVMASFERVLMPGLEKNQYSILWVEHQDKGRLE
                     LNFVIPNMELQTGKRLQPYYDRADRPRIDAWQTLVNHHYGLHDPNAPENRRTLTLPDNL
                     PETKQALAESVTRGLEVLYHSGEIKGRQDVIQALTEAGLDVVRVTRSSISIADPNGGRN
                     IRLKGAFYEQSFTDGRGVREKAERESRIYRENAERRIQQARRICKRGCDLKRDRKSKSL
                     "
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            105..383
                     /locus_tag="IQS19_RS25295"
     CDS             105..383
                     /locus_tag="IQS19_RS25295"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="WP_251326745.1"
                     /translation="MLKLAGNTGMMLLGIVFLLFTASGGTLWYLGWRIQANLEDIRKQE
                     ETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVISFQGKEWVHLKE"
                     /name="mobilization protein"
     gene            390..623
                     /locus_tag="IQS19_RS24505"
                     /old_locus_tag="IQS19_24515"
     CDS             390..623
                     /locus_tag="IQS19_RS24505"
                     /old_locus_tag="IQS19_24515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_029401705.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSERTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(936..1217)
                     /locus_tag="IQS19_RS24510"
                     /old_locus_tag="IQS19_24520"
     CDS             complement(936..1217)
                     /locus_tag="IQS19_RS24510"
                     /old_locus_tag="IQS19_24520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000786945.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024177387.1"
                     /translation="MKNEDDYKTGWTTQTTNPATGKKCSGGAARNLRIYQAGGANSVRV
                     KAAIEGVQSIQPIIDMQQSQIEQQQTQIAMLTQSLSQAINELTKSRNQ"
                     /name="hypothetical protein"
     gene            complement(1227..1484)
                     /locus_tag="IQS19_RS24515"
                     /old_locus_tag="IQS19_24525"
     CDS             complement(1227..1484)
                     /locus_tag="IQS19_RS24515"
                     /old_locus_tag="IQS19_24525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001508827.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001508827.1"
                     /translation="MPKKTSKPNDLSNTINNIKKEINSGFTELLNRVEALEASDAQHSM
                     AIRDLQIQARAARGDKRMDIARDFGLSEGRISQIVNAGRN"
                     /name="hypothetical protein"
     gene            2029..2739
                     /locus_tag="IQS19_RS24520"
                     /old_locus_tag="IQS19_24530"
     CDS             2029..2739
                     /locus_tag="IQS19_RS24520"
                     /old_locus_tag="IQS19_24530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000967646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_024177388.1"
                     /translation="MLYWKRMPSLWIGIKISEFNDLDTAKAIAALKIYLTFCLFCKESD
                     SGQRTVELTFSNLCEIASLSRSLVNEGLKILYAKELIKNLSTTVRKKIYTIDVLEKHDD
                     GWCKLPFKGIVGEDGKISAFQSMHNRYPFELLALQTYMYLLYARDNRNEYTLARKKTIC
                     KKLKCKLPELNKAITYLIHIGLLDRIVKKSIENKPLEMFHDSCYFYFRAGSNSALTYKR
                     KSEVLNLSEEDLPF"
                     /name="hypothetical protein"
     gene            complement(2851..3366)
                     /locus_tag="IQS19_RS24525"
                     /old_locus_tag="IQS19_24535"
     CDS             complement(2851..3366)
                     /locus_tag="IQS19_RS24525"
                     /old_locus_tag="IQS19_24535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000675352.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
                     /protein_id="WP_094198730.1"
                     /translation="MKFYTISSSYIKYLKDFDDKVPNSEDPTYNNPKAFIGIVLEIEGH
                     KYLAPLTSPKAWHANVKESSPAFFKLHENGVPDNQLGLINLKFMIPIIEAEVSLLDLDS
                     MPDTPYKRMLYKQLQFIRVNEDKISEKSKLLRNLALQGRMQRTCDFAVLEEKYQHFGKK
                     PEDMEIDD"
                     /name="type III toxin-antitoxin system ToxN/AbiQ family
                     toxin"
     gene            complement(4651..4842)
                     /locus_tag="IQS19_RS24530"
                     /old_locus_tag="IQS19_24540"
     CDS             complement(4651..4842)
                     /locus_tag="IQS19_RS24530"
                     /old_locus_tag="IQS19_24540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165987.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGETL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4907..5230
                     /locus_tag="IQS19_RS24535"
                     /old_locus_tag="IQS19_24545"
     CDS             4907..5230
                     /locus_tag="IQS19_RS24535"
                     /old_locus_tag="IQS19_24545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000955993.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001749507.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQGAR
                     DDC"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          4489..4570
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(3672..4189)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.792"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3..700
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="87.449"
                     /coverage="99.0"
                     /evalue="5.39e-103"
     Typing          4875..5224
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.162"
                     /coverage="99.0"
                     /evalue="1.7700000000000002e-64"
     Typing          5221..6041
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.35"
                     /coverage="99.0"
                     /evalue="1.55e-176"
ORIGIN
        1 cgaaaatcaa agtcgctata gcccggttta cggcctcgac ggaggaatcg ctggaaaaac
       61 accgggaagg ggtgaaagag gcgatgatgc agcacaggag ggacgtgtta aagctggcag
      121 ggaatacggg catgatgtta ctggggatag tctttctcct gtttaccgcg agtggcggga
      181 cgctctggta tcttggctgg aggatacagg cgaacctgga agatatcagg aagcaggaag
      241 agacattaca gaaactgaac gcgaagacat ggggcgtgga gtttgtgcag gacgggaaca
      301 ggaaatttct ggtccttcct tacgggaagt cagcagaggt gatttccttt caggggaagg
      361 aatgggtaca tctgaaggag tgacacagag tgacagagct ggaaacacat ttgctgaacg
      421 ccttagagca gctgcaacag gactatatgc agcggctgag cgaatgggag agcgccttcg
      481 tggaattgca gaagatgttt tcgcttacgc aacgggacaa cgcgatgctg aacgagcggg
      541 tcatgcagtt gagtcagcag gtgcagcact tgagcgagcg gacagaacgc ttgagccagt
      601 tatacagcga gaactggaga taagagagga acggttgata catgagcgcg aacatgcgtt
      661 atccctggaa cgggaacgca cgctggatgg tccttcgttg tcgctgtgat ggcgaaacta
      721 taaaaaatgg cagattcagt ggattttgac gggctaatgt agtctgcacc atctggttgc
      781 atagatattc atacggttaa aatttatcag gcgcgatcgc ggtagctttt cgggtgattt
      841 gttgttggtt ttggctgact gccgccccgt tcgcggcgaa gctgtccggg gcggtgcggg
      901 caacggatgt tatggtaaat aacatccttt atagcctatt gattcctgct ttttgttagc
      961 tcattgattg cctgagacaa agattgagtc agcattgcta tttgagtttg ttgttgctcg
     1021 atttgtgact gttgcatatc gatgattggc tgtattgact ggacaccctc gattgcagct
     1081 tttacccgca cggagtttgc tccaccggct tgatatatcc ttaagtttct ggctgcgcct
     1141 ccagaacatt ttttccctgt tgccgggttt gttgtctgag tcgtccatcc tgttttgtag
     1201 tcgtcttcat ttttcataag tctgtcttag ttacgacccg cattaacgat ctggctaatt
     1261 cgtccctcgc taaggccaaa gtctcttgct atatccatgc gcttgtctcc gcgagcggct
     1321 ctagcctgaa tttgtaaatc acgtatcgcc atgctgtgtt gtgcgtcact agcctctaag
     1381 gcttctacgc gattaagtaa ctcagtaaaa cctgagttaa tttctttctt tatgttgttg
     1441 atagtgttgc ttaaatcgtt tggttttgat gtttttttag gcatggcata tttctctata
     1501 ctcggcggct aagtccgcta aagattttta gttttgttaa agttgtaagg tagggattat
     1561 tgctcctttt ggcaaggtga atttaatgag ataaagaaat ttagtgcttt atgcagggtg
     1621 gcttgcaagg cacaacgctt tgtttgttct gatctaaagt cctaatgtga aaacatttaa
     1681 cgtaaccaga aaagcatcag cactgcattt acggttcacc atgaaccata atatgatttc
     1741 taagaatacc aaaagcaaga taaaatatct tatataacat atagatacct ttcttttgcc
     1801 ttatcttatc tttctagata gatttttgtg aaggcgttac aacgccttca cagcctgaga
     1861 taatcaaaaa aacaaagcta tcaggaggga taaaaaatgt ttgagaaagg tgtgtttttg
     1921 gctgaaaggc ttgcgaaggt cgcagtggtg ctaactaatc tggtgctatc tatgtctgta
     1981 ttggggttgg tctatttcat ttttcaaatt ctgggaatga ggtgatttat gctgtactgg
     2041 aaaagaatgc cttcactatg gataggtatc aaaatatctg aattcaacga tcttgataca
     2101 gcaaaagcca tcgccgcgtt aaagatttat ttaacatttt gccttttctg caaagagtca
     2161 gattcaggac agagaactgt tgagctaact tttagtaacc tatgtgagat agcatcatta
     2221 agccgatcgt tagttaacga agggcttaaa attctttatg caaaagagtt gataaaaaat
     2281 ttatcaacga cagtacgtaa aaaaatttat accatagatg tattagagaa gcatgatgat
     2341 ggttggtgta agcttccctt taaaggaatt gtaggtgaag atggaaaaat aagtgcattt
     2401 caatccatgc acaacagata tccatttgag ttgctagctt tacaaaccta catgtacctt
     2461 ctttatgctc gagataatag aaatgagtat actcttgcca ggaaaaaaac aatatgtaaa
     2521 aaactgaaat gcaaactacc tgaactaaat aaagctatta cctatcttat tcatatcggt
     2581 ttacttgata ggattgttaa aaaatcaata gaaaacaagc cgttggaaat gtttcatgat
     2641 tcatgttact tctactttag agcgggaagt aacagcgctc tcacttacaa aaggaaatca
     2701 gaggtgctta atctttcaga ggaggacttg cctttttgat tgcttctcga aatcaaaatt
     2761 agaatatctc attcttatat tggatgagag caaaaaaaat aggtccaaaa ccgcttgatt
     2821 ttggaccttc aattccataa aaaagaatgg ttaatcgtct atttccatgt cttcaggttt
     2881 tttaccgaaa tgttgatatt tttcttctaa cacggcaaag tcgcatgttc tttgcattct
     2941 gccttgcaag gcaaggtttc ttaatagttt tgatttttca gatattttat cttcatttac
     3001 acgaataaat tgtaactgtt tatatagcat tcttttgtaa ggcgtatcag gcatgctatc
     3061 cagatcaagt aaagacactt cagcttcgat tattggaatc ataaatttca gattaatcaa
     3121 tccaagctga ttatcaggga caccgttttc atgaagtttg aagaaggcgg gtgatgactc
     3181 ttttacatta gcatgccatg cttttggcga tgttaaaggt gctaaatatt tatgtccttc
     3241 aatctctagt actatgccaa tgaaagcctt aggattgttg tatgtaggat cttcgctatt
     3301 gggaactttg tcatcaaagt ccttcaggta ttttatgtaa ctgcttgata ttgtgtaaaa
     3361 tttcattttt ttctcgtaaa aaaggcgact gtgtatagtc gcctttttta ctttattact
     3421 ttaaggtagt aaatgaccta aatttctagc tgcacttaaa ggtagcaaat cacctgaatt
     3481 tctagctgca cttaaaggta gcaaatcacc tgaatttcta gctgcactta aaggtagcaa
     3541 atcacctaaa tttctagctg cacttaaagg tagcaaatca ccttgaacta agtatacatg
     3601 atcttcgctt gggcttacaa ctaggtgctt agcatgggat gttcagtcaa atgacggcac
     3661 taatcaaaag gatcttcttg agatcatctt tttctgcgcg taatctcttg gtctgaaaac
     3721 ggaaaaacca cccggcaagg tggttttttc gaaggttcag taaaccggca agtttctgga
     3781 ccgtggtaac tggctttcgc agagcacagc aaccaaatct gtccttccag tgtagccgta
     3841 ctgaggcgca cacttcaaga gcaacctcgt gtttagctaa caaatcatct gcgaaccaag
     3901 ttaccaatgg ctgctgccag tggcgctttg tcgtgtcttt ccggtttgga ctcaagtgga
     3961 tagttaccgg ataaggcgca gcagtcggac tgaacggggg gttcgtgcat acagtccagc
     4021 ttggagcgaa ctgcctaccc ggaaccgagt gtcaggcgtg gaatgagata aacgcggcca
     4081 taacagcgga gtgacaccgg taaaccgaat ggcaggaaca ggagagcgca cgagggagcc
     4141 accaggggga aacgcctggt atctttaagt cctgtcgggt ttcgccacct ctgacttgag
     4201 cgtcggtttt tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc cagcggtgtg
     4261 gccttttccg ggttcttgtt ttttgctcac atgtttcttt tggtgttatc ccctgattct
     4321 gtggataacc gcattaccgt ttttgagtga gctgataccg ctcgccgcag ccgaacgacc
     4381 gagcgtagcg agtcagtgag cgaggaagcg gaagagcgtc tgatgctgca ttttctcctt
     4441 acgcatctgt gcggcatttc acacccggca tggcgcactt ttcatacaat ctgcactgat
     4501 gccgcatggt taagccagta tacactccgc tatcgctacg tgactggttc agggcttcgc
     4561 cccgaaaccc cctgacgcgc cctgacgggc ttgtctgctc ccggcatccg ctcacagaca
     4621 agctgtgacc gtctccggga gctgcttgtg tcagagggtt tcaccgtcat ccccgaagcg
     4681 tgcgaggcag ctgcggtaaa gctcatcggc gtggtcgtga agagattcac agatgtctgc
     4741 ctgttcatcc gcgtccagtt cgttgagttt ctccagcagc gttaatgtct ggcttctgat
     4801 aaagcgggcc atgttaaggg cggttttttc ctgtttagtc actgatgcct ccgtgtaagg
     4861 gggatttctg ttcatggggg taatgatacc gatgaaacgc gagaggatgc tcacgatacg
     4921 ggttactgat gatgaacatg cccggttact ggaacgctgt gagggtaaac aactggcggt
     4981 atggatgcgg cgggtctgcc tgggtgagcc ggttgcccgt tccgggaagc tgccgacact
     5041 ggcaccgccg ttactgcgtc agctggctgc catcgggaat aaccttaatc agacggcgag
     5101 gaaggtgaac agcgggcagt ggtcttccgg tgaccgggtt caggtggtgg ccgcactgat
     5161 ggccatcgag agagagttgc gcagcttacg gcaggtcgtc agggaacagg gagcgcggga
     5221 tgattgttaa atttcatgcc aggggaaaag gcggtggcag tggtccggtt gattacctgc
     5281 tgggaaggga gcgaaaccgg gaaggcgcaa cggtgcttca gggtaatccg gaagaagtcc
     5341 gggaactcat cgatgccacg ccatttgcga agaaatacac gtcgggtgtt ctgtcgttcg
     5401 cggagaagga gctgccgccg ggagggcgtg aaaaggtgat ggcgagtttt gagcgtgtac
     5461 tgatgcccgg tctcgaaaag aatcagtaca gcatcctgtg ggtggagcac caggacaagg
     5521 gacggcttga gctaaatttt gtcattccga acatggagct acagaccgga aaacgcctcc
     5581 agccgtacta cgaccgggca gacaggccga gaattgatgc ctggcagacg ctggtgaatc
     5641 accattacgg gctgcatgac cccaacgccc cggagaaccg caggacgctg acactccctg
     5701 ataacctgcc ggaaacgaaa caggcgcttg ctgagagcgt tacacgaggt ctggaggtgc
     5761 tttaccattc cggagagata aaaggccgtc aggatgtgat tcaggcgctc acagaggcgg
     5821 ggcttgacgt ggtcagggtg acgcgaagca gtatcagcat tgcagacccg aacggcggga
     5881 ggaatatcag actgaaagga gcgttttatg agcaatcttt tacggacggg cgcggagttc
     5941 gagaaaaagc tgaaagagag agccgaatct acagagaaaa tgctgaacga cgaattcagc
     6001 aggctcggcg aatctgtaag cgaggctgtg acctcaaacg agac
//
